The recent advances in single-cell technologies have enabled us to profile genomic features at unprecedented resolution and datasets from multiple domains are available, including datasets that profile different types of genomic features and datasets that profile the same type of genomic features across different species. These datasets typically have different powers in identifying the unknown cell types through clustering, and data integration can potentially lead to a better performance of clustering algorithms. In this work, we formulate the problem in an unsupervised transfer learning framework, which utilizes knowledge learned from auxiliary dataset to improve the clustering performance of target dataset. The degree of shared information among the target and auxiliary datasets can vary, and their distributions can also be different. To address these challenges, we propose an elastic coupled co-clustering based transfer learning algorithm, by elastically propagating clustering knowledge obtained from the auxiliary dataset to the target dataset. Implementation on single-cell genomic datasets shows that our algorithm greatly improves clustering performance over the traditional learning algorithms. The source code and data sets are available at https://github.com/cuhklinlab/elasticC3.
Time course microarray data provide insight about dynamic biological processes. While several clustering methods have been proposed for the analysis of these data structures, comparison and selection of appropriate clustering methods are seldom discussed. We compared $3$ probabilistic based clustering methods and $3$ distance based clustering methods for time course microarray data. Among probabilistic methods, we considered: smoothing spline clustering also known as model based functional data analysis (MFDA), functional clustering models for sparsely sampled data (FCM) and model-based cluste…
Adjacency-constrained hierarchical clustering of a band similarity matrix with application to Genomics
Université d’Evry Val d’Essonne（埃夫里-瓦勒德埃松大学）；Hyphen-stat；Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA（巴黎萨克雷植物科学研究所）；MIAT, Université de Toulouse, INRA（农业生物技术研究所，图卢兹大学）
The prediction of phenotypic traits using high-density genomic data has many applications such as the selection of plants and animals of commercial interest; and it is expected to play an increasing role in medical diagnostics. Statistical models used for this task are usually tested using cross-validation, which implicitly assumes that new individuals (whose phenotypes we would like to predict) originate from the same population the genomic prediction model is trained on. In this paper we propose an approach based on clustering and resampling to investigate the effect of increasing genetic di…
We propose an algorithm for clustering high dimensional data. If $P$ features for $N$ objects are represented in an $N\times P$ matrix ${\bf X}$, where $N\ll P$, the method is based on exploiting the cluster-dependent structure of the $N\times N$ matrix ${\bf XX}^T$. Computational burden thus depends primarily on $N$, the number of objects to be clustered, rather than $P$, the number of features that are measured. This makes the method particularly useful in high dimensional settings, where it is substantially faster than a number of other popular clustering algorithms. Aside from an upper bou…
Clustering methods have led to a number of important discoveries in bioinformatics and beyond. A major challenge in their use is determining which clusters represent important underlying structure, as opposed to spurious sampling artifacts. This challenge is especially serious, and very few methods are available, when the data are very high in dimension. Statistical Significance of Clustering (SigClust) is a recently developed cluster evaluation tool for high dimensional low sample size data. An important component of the SigClust approach is the very definition of a single cluster as a subset…
Feature selection is an important and challenging task in high dimensional clustering. For example, in genomics, there may only be a small number of genes that are differentially expressed, which are informative to the overall clustering structure. Existing feature selection methods, such as Sparse K-means, rarely tackle the problem of accounting features that can only separate a subset of clusters. In genomics, it is highly likely that a gene can only define one subtype against all the other subtypes or distinguish a pair of subtypes but not others. In this paper, we propose a K-means based c…
Unsupervised continual learning remains a relatively uncharted territory in the existing literature because the vast majority of existing works call for unlimited access of ground truth incurring expensive labelling cost. Another issue lies in the problem of task boundaries and task IDs which must be known for model's updates or model's predictions hindering feasibility for real-time deployment. Knowledge Retention in Self-Adaptive Deep Continual Learner, (KIERA), is proposed in this paper. KIERA is developed from the notion of flexible deep clustering approach possessing an elastic network st…
ShanghaiTech University（上海科技大学）；The Chinese University of Hong Kong（香港中文大学）
Modern high-throughput sequencing technologies have enabled us to profile multiple molecular modalities from the same single cell, providing unprecedented opportunities to assay celluar heterogeneity from multiple biological layers. However, the datasets generated from these technologies tend to have high level of noise and are highly sparse, bringing challenges to data analysis. In this paper, we develop a novel information-theoretic co-clustering-based multi-view learning (scICML) method for multi-omics single-cell data integration. scICML utilizes co-clusterings to aggregate similar feature…
In recent biomedical scientific problems, it is a fundamental issue to integratively cluster a set of objects from multiple sources of datasets. Such problems are mostly encountered in genomics, where data is collected from various sources, and typically represent distinct yet complementary information. Integrating these data sources for multi-source clustering is challenging due to their complex dependence structure including directional dependency. Particularly in genomics studies, it is known that there is certain directional dependence between DNA expression, DNA methylation, and RNA expre…
Motivation: Gene set testing is typically performed in a supervised context to quantify the association between groups of genes and a clinical phenotype. In many cases, however, a gene set-based interpretation of genomic data is desired in the absence of a phenotype variable. Although methods exist for unsupervised gene set testing, they predominantly compute enrichment relative to clusters of the genomic variables with performance strongly dependent on the clustering algorithm and number of clusters. Results: We propose a novel method, spectral gene set enrichment (SGSE), for unsupervised com…
Johns Hopkins University（约翰斯·霍普金斯大学）；Beijing University of Posts and Telecommunications（北京邮电大学）
State-of-the-art subspace clustering methods are based on expressing each data point as a linear combination of other data points while regularizing the matrix of coefficients with $\ell_1$, $\ell_2$ or nuclear norms. $\ell_1$ regularization is guaranteed to give a subspace-preserving affinity (i.e., there are no connections between points from different subspaces) under broad theoretical conditions, but the clusters may not be connected. $\ell_2$ and nuclear norm regularization often improve connectivity, but give a subspace-preserving affinity only for independent subspaces. Mixed $\ell_1$, …
Unsupervised clustering of curves according to their shapes is an important problem with broad scientific applications. The existing model-based clustering techniques either rely on simple probability models (e.g., Gaussian) that are not generally valid for shape analysis or assume the number of clusters. We develop an efficient Bayesian method to cluster curve data using an elastic shape metric that is based on joint registration and comparison of shapes of curves. The elastic-inner product matrix obtained from the data is modeled using a Wishart distribution whose parameters are assigned car…
The University of Melbourne（墨尔本大学）；Deakin University（迪肯大学）；Data61, CSIRO（联邦科学与工业研究组织Data61）
Subspace clustering aims to find groups of similar objects (clusters) that exist in lower dimensional subspaces from a high dimensional dataset. It has a wide range of applications, such as analysing high dimensional sensor data or DNA sequences. However, existing algorithms have limitations in finding clusters in non-disjoint subspaces and scaling to large data, which impinge their applicability in areas such as bioinformatics and the Internet of Things. We aim to address such limitations by proposing a subspace clustering algorithm using a bottom-up strategy. Our algorithm first searches for…
Distributional Reduction: Unifying Dimensionality Reduction and Clustering with Gromov-Wasserstein
ENS de Lyon, CNRS, UMPA UMR 5669（里昂大学、国家科学研究中心、UMPA UMR 5669）；EPFL, LTS4（苏黎世联邦理工学院、LTS4）；Université Bretagne Sud, IRISA UMR 6074（布列塔尼南部大学、IRISA UMR 6074）；École polytechnique, Institut Polytechnique de Paris, CMAP UMR 7641（巴黎高等学院、巴黎理工学院、CMAP UMR 7641）；Inria, ENS de Lyon, CNRS, Université Claude Bernard Lyon 1, LIP UMR 5668（法国国家科学研究中心、里昂大学、 Claude Bernard Lyon 1 大学、LIP UMR 5668）
University of Oxford（牛津大学）；Alan Turing Institute（艾伦·图灵研究所）；University of Birmingham（伯明翰大学）；University of Manchester（曼彻斯特大学）
Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box approach to dimensionality reduction does not provide sufficient insights. Common data analysis workflows additionally use clustering techniques to identify groups of similar features. This usually leads to a two-stage process, however, it would be desirable to construct a joint modelling framework for simultaneous dimensionality reduction and clustering of feat…
We propose a method for estimating coefficients in multivariate regression when there is a clustering structure to the response variables. The proposed method includes a fusion penalty, to shrink the difference in fitted values from responses in the same cluster, and an L1 penalty for simultaneous variable selection and estimation. The method can be used when the grouping structure of the response variables is known or unknown. When the clustering structure is unknown the method will simultaneously estimate the clusters of the response and the regression coefficients. Theoretical results are p…
Stanford University（斯坦福大学）；Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Clustering is a ubiquitous task in data science. Compared to the commonly used $k$-means clustering, $k$-medoids clustering requires the cluster centers to be actual data points and support arbitrary distance metrics, which permits greater interpretability and the clustering of structured objects. Current state-of-the-art $k$-medoids clustering algorithms, such as Partitioning Around Medoids (PAM), are iterative and are quadratic in the dataset size $n$ for each iteration, being prohibitively expensive for large datasets. We propose BanditPAM, a randomized algorithm inspired by techniques from…
High-order clustering aims to identify heterogeneous substructures in multiway datasets that arise commonly in neuroimaging, genomics, social network studies, etc. The non-convex and discontinuous nature of this problem pose significant challenges in both statistics and computation. In this paper, we propose a tensor block model and the computationally efficient methods, \emph{high-order Lloyd algorithm} (HLloyd), and high-order spectral clustering (HSC), for high-order clustering. The convergence guarantees and statistical optimality are established for the proposed procedure under a mild sub…
University of Massachusetts Amherst（马萨诸塞大学阿默斯特分校）；National Institute of Standards and Technology（美国国家标准与技术研究院）；New York University（纽约大学）
Hierarchical clustering is a fundamental task often used to discover meaningful structures in data, such as phylogenetic trees, taxonomies of concepts, subtypes of cancer, and cascades of particle decays in particle physics. Typically approximate algorithms are used for inference due to the combinatorial number of possible hierarchical clusterings. In contrast to existing methods, we present novel dynamic-programming algorithms for \emph{exact} inference in hierarchical clustering based on a novel trellis data structure, and we prove that we can exactly compute the partition function, maximum …
Nowadays, clinical research routinely uses omics data, such as gene expression, for predicting clinical outcomes or selecting markers. Additionally, so-called co-data are often available, providing complementary information on the covariates, like p-values from previously published studies or groups of genes corresponding to pathways. Elastic net penalisation is widely used for prediction and covariate selection. Group-adaptive elastic net penalisation learns from co-data to improve the prediction and covariate selection, by penalising important groups of covariates less than other groups. Exi…
We present a nonparametric Bayesian method for disease subtype discovery in multi-dimensional cancer data. Our method can simultaneously analyse a wide range of data types, allowing for both agreement and disagreement between their underlying clustering structure. It includes feature selection and infers the most likely number of disease subtypes, given the data. We apply the method to 277 glioblastoma samples from The Cancer Genome Atlas, for which there are gene expression, copy number variation, methylation and microRNA data. We identify 8 distinct consensus subtypes and study their prognos…
Clustering has long been a popular unsupervised learning approach to identify groups of similar objects and discover patterns from unlabeled data in many applications. Yet, coming up with meaningful interpretations of the estimated clusters has often been challenging precisely due to its unsupervised nature. Meanwhile, in many real-world scenarios, there are some noisy supervising auxiliary variables, for instance, subjective diagnostic opinions, that are related to the observed heterogeneity of the unlabeled data. By leveraging information from both supervising auxiliary variables and unlabel…
In mixed multi-view data, multiple sets of diverse features are measured on the same set of samples. By integrating all available data sources, we seek to discover common group structure among the samples that may be hidden in individualistic cluster analyses of a single data-view. While several techniques for such integrative clustering have been explored, we propose and develop a convex formalization that will inherit the strong statistical, mathematical and empirical properties of increasingly popular convex clustering methods. Specifically, our Integrative Generalized Convex Clustering Opt…
The clustering of data into physically meaningful subsets often requires assumptions regarding the number, size, or shape of the subgroups. Here, we present a new method, simultaneous coherent structure coloring (sCSC), which accomplishes the task of unsupervised clustering without a priori guidance regarding the underlying structure of the data. sCSC performs a sequence of binary splittings on the dataset such that the most dissimilar data points are required to be in separate clusters. To achieve this, we obtain a set of orthogonal coordinates along which dissimilarity in the dataset is maxi…
In most gene expression data, the number of training samples is very small compared to the large number of genes involved in the experiments. However, among the large amount of genes, only a small fraction is effective for performing a certain task. Furthermore, a small subset of genes is desirable in developing gene expression based diagnostic tools for delivering reliable and understandable results. With the gene selection results, the cost of biological experiment and decision can be greatly reduced by analyzing only the marker genes. An important application of gene expression data in func…
Cluster Analysis with Resampling for Validation and Exploration (CARVE)
Department of Statistics, Columbia University, New York, NY, USA（哥伦比亚大学统计学系）；Center for Theoretical Neuroscience, Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA（哥伦比亚大学理论神经科学中心、Zuckerman思维-大脑-行为研究所）；Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN, USA（诺丁汉大学应用与计算数学与统计学系）；School of Data and Information Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA（北卡罗来纳大学夏洛特分校数据与信息科学学院）；Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA（哥伦比亚大学癌症动力学伊万·里弗斯研究所）
